rbbt-marq 1.0.0 → 1.0.1

data/R/CustomDS.R

@@ -4,17 +4,26 @@ CustomDS.process <- function(prefix, cross_platform, conditions, description, tw
     # Read data
     genes = scan(file=paste(prefix,'codes',sep = "/"), what=character(),sep="\n",quiet=T);
     m = matrix(scan(file=paste(prefix,'values',sep = "/"), sep="\t",quiet=T),length(genes),byrow=T);
+    str(m);
+    str(genes);
     rownames(m) <- genes
 
+   
     # Read conditions
     conditions.list = vector();
     names = vector();
+    str(conditions)
     for (file in conditions){
-      values = scan(paste(prefix,file,sep="/"),what=character(),sep="\n",quiet=T)
+      str(paste(prefix,file,sep="/"));
+      values = scan(paste(prefix,file,sep="/"),what=character(), sep = "\n")
       names = c(names, file)
+      str(values)
       conditions.list = cbind(conditions.list, values)
     }
 
+    colnames(conditions.list) <- names;
+    str(conditions.list)
+
 
 
 
@@ -39,7 +48,6 @@ CustomDS.process <- function(prefix, cross_platform, conditions, description, tw
     if (cross_platform){
       prefix = paste(prefix,'cross_platform', sep="_")
     }
-    colnames(conditions.list) <- names;
 
     values <- MA.process(m, conditions.list, two.channel);
 

data/install_scripts/GEO/Rakefile

@@ -164,7 +164,7 @@ end
 
 task 'annotate_Words' do
   require 'MARQ/annotations'
-  require 'rbbt/util/misc'
+  require 'rbbt/bow/bow'
   annotations('Words'){|dataset|
     terms = {}
     description = Open.read(GEO.dataset_path(dataset) + '.description')

data/lib/MARQ/CustomDS.rb

@@ -1,6 +1,7 @@
 require 'rbbt/util/open'
 require 'MARQ'
 require 'MARQ/ID'
+
 module CustomDS
   @@r = nil
 
@@ -9,6 +10,7 @@ module CustomDS
   end
 
   def self.r
+    require 'rsruby'
     if @@r.nil?
       RSRuby.instance.source(MARQ.rootdir + '/R/MA.R')
       RSRuby.instance.source(MARQ.rootdir + '/R/CustomDS.R')
@@ -62,10 +64,7 @@ module CustomDS
     Dir.glob(File.join(customdir, org) + '/*.orders').collect{|f| clean(File.basename(f.sub(/.orders/,'')))}.uniq
   end
 
-  def self.process(name)
-    puts "Processing #{ name }"
-    org = organism(name)
-    prefix = File.join(customdir, org, name)
+  def self.process_matrix(prefix, org)
     conditions = Dir.glob(prefix + '/*').collect{|f| File.basename(f)} - %w(values codes info description cross_platform)
     description = Open.read(File.join(prefix, 'description'))
 
@@ -82,6 +81,14 @@ module CustomDS
     end
   end
 
+  def self.process(name)
+    puts "Processing #{ name }"
+    org = organism(name)
+    prefix = File.join(customdir, org, name)
+
+    CustomDS::process_matrix(prefix, org)
+  end
+
 end
 
 
@@ -89,6 +96,7 @@ if __FILE__ == $0
   p CustomDS::datasets('sgd')
   p CustomDS::path('HaploidData')
   p CustomDS::path('HaploidData_cross_platform')
+
   exit
 
   org = 'sgd'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-marq
 version: !ruby/object:Gem::Version 
-  version: 1.0.0
+  version: 1.0.1
 platform: ruby
 authors: 
 - Miguel Vazquez